%0 Journal Article %1 ISI:000256000700007 %A Lee, Jinhyuk %A Shin, Seokmin %C 635-4 YEOGSAM-DONG, KANGNAM-GU, SEOUL 135-703, SOUTH KOREA %D 2008 %I KOREAN CHEMICAL SOC %J BULLETIN OF THE KOREAN CHEMICAL SOCIETY %K beta-hairpin core energy free hydrophobic %N 4 %P 741-748 %T Understanding beta-hairpin formation: Computational studies for three different hairpins %V 29 %X We have studied the folding mechanism of beta-hairpins in the proteins 1GB1, 3AIT and 1A2P by conducting unfolding simulations at moderately high temperatures. The analysis of trajectories obtained from molecular dynamics simulations in explicit aqueous solution suggests that the positions of the hydrophobic core residues lead to subtle differences in the details of folding dynamics. However, the folding of three different hairpins can be explained by a unified mechanism that is a blend of the hydrogen-bond-centric and the hydrophobic-centric models. The initial stage of beta-hairpin folding involves various partially folded intermediate structures which are stabilized by both the van der Waals interactions of hydrophobic core residues and the electrostatic interactions of non-native hydrogen bonds. The native structure is obtained by forming native contacts in the final tune-up process. Depending on the relative positions of the hydrophobic residues, the actual mechanism of hairpin folding may or may not exhibit well-defined intermediates.

@article{ISI:000256000700007, abstract = {{We have studied the folding mechanism of beta-hairpins in the proteins 1GB1, 3AIT and 1A2P by conducting unfolding simulations at moderately high temperatures. The analysis of trajectories obtained from molecular dynamics simulations in explicit aqueous solution suggests that the positions of the hydrophobic core residues lead to subtle differences in the details of folding dynamics. However, the folding of three different hairpins can be explained by a unified mechanism that is a blend of the hydrogen-bond-centric and the hydrophobic-centric models. The initial stage of beta-hairpin folding involves various partially folded intermediate structures which are stabilized by both the van der Waals interactions of hydrophobic core residues and the electrostatic interactions of non-native hydrogen bonds. The native structure is obtained by forming native contacts in the final tune-up process. Depending on the relative positions of the hydrophobic residues, the actual mechanism of hairpin folding may or may not exhibit well-defined intermediates.}}, added-at = {2009-01-04T03:17:32.000+0100}, address = {{635-4 YEOGSAM-DONG, KANGNAM-GU, SEOUL 135-703, SOUTH KOREA}}, affiliation = {{Shin, S (Reprint Author), Seoul Natl Univ, Sch Chem, Seoul 151747, South Korea. {[}Lee, Jinhyuk; Shin, Seokmin] Seoul Natl Univ, Sch Chem, Seoul 151747, South Korea.}}, author = {Lee, Jinhyuk and Shin, Seokmin}, author-email = {{sshin@snu.ac.kr}}, biburl = {https://www.bibsonomy.org/bibtex/26cc523d22280d1cde09acc6f2bd1e2c8/huiyangsfsu}, cited-references = {{BERENDSEN HJC, 1984, J CHEM PHYS, V81, P3684. BLANCO F, 1998, CURR OPIN STRUC BIOL, V8, P107. BOCZKO EM, 1995, SCIENCE, V269, P393. BONVIN AMJJ, 2000, J MOL BIOL, V296, P255. BROOKS BR, 1983, J COMPUT CHEM, V4, P187. DINNER AR, 1999, P NATL ACAD SCI USA, V96, P9068. GALZITSKAYA OV, 2002, CURR PROTEIN PEPT SC, V3, P191. GARCIA AE, 2001, PROTEINS, V42, P345. JANG S, 2002, J AM CHEM SOC, V124, P4976. JANG SM, 2003, J AM CHEM SOC, V125, P14841, DOI 10.1021/ja034701i. KIM MG, 2007, KOREAN CHEM SOC, V28, P1151. KLIMOV DK, 2000, P NATL ACAD SCI USA, V97, P2544. LEE J, 2001, BIOPHYS J, V81, P2507. LEE J, 2002, J PHYS CHEM B, V106, P8796, DOI 10.1021/jp0141732. LEE J, 2003, B KOR CHEM SOC, V24, P785. MA BY, 2000, J MOL BIOL, V296, P1091. MA BY, 2003, PROTEIN SCI, V12, P1882, DOI 10.1110/ps.0306103. MUFIOZ V, 1995, CURR OPIN BIOTECH, V6, P382. MUNOZ V, 1995, CURR OPIN BIOTECH, V6, P382. PANDE VS, 1999, P NATL ACAD SCI USA, V96, P9062. PREVOST M, 1997, PROTEINS, V29, P212. RYCKAERT JP, 1977, J COMPUT PHYS, V23, P327. THOMPSON PA, 1997, BIOCHEMISTRY-US, V36, P9200. VRIEND G, 1990, J MOL GRAPHICS, V8, P52. WILLIAMS S, 1996, BIOCHEMISTRY-US, V35, P691. ZAGROVIC B, 2001, J MOL BIOL, V313, P151. ZHOU RH, 2001, P NATL ACAD SCI USA, V98, P14931. ZHOU YQ, 2002, PROTEINS, V47, P154.}}, doc-delivery-number = {{302WM}}, interhash = {9dd97a348d247a7f105d5080e2c4ec69}, intrahash = {6cc523d22280d1cde09acc6f2bd1e2c8}, issn = {{0253-2964}}, journal = {{BULLETIN OF THE KOREAN CHEMICAL SOCIETY}}, journal-iso = {{Bull. Korean Chem. Soc.}}, keywords = {beta-hairpin core energy free hydrophobic}, keywords-plus = {{MOLECULAR-DYNAMICS SIMULATIONS; ENERGY LANDSCAPE; PROTEIN-G; HELIX; FRAGMENT; PEPTIDE; STABILITY; MODEL; KINETICS; PROGRAM}}, language = {{English}}, month = {{APR 20}}, number = {{4}}, number-of-cited-references = {{28}}, pages = {{741-748}}, publisher = {{KOREAN CHEMICAL SOC}}, subject-category = {{Chemistry, Multidisciplinary}}, times-cited = {{0}}, timestamp = {2009-01-04T03:17:32.000+0100}, title = {{Understanding beta-hairpin formation: Computational studies for three different hairpins}}, type = {{Article}}, unique-id = {{ISI:000256000700007}}, volume = {{29}}, year = {{2008}} }